title: Binding of NF-κB to nucleosomes: effect of translational positioning, nucleosome remodeling and linker histone H1.
abstract: NF-κB is a key transcription factor regulating the expression of inflammatory responsive genes. How NF-κB binds to naked DNA templates is well documented, but how it interacts with chromatin is far from being clear. Here we used a combination of UV laser footprinting, hydroxyl footprinting and electrophoretic mobility shift assay to investigate the binding of NF-κB to nucleosomal templates. We show that NF-κB p50 homodimer is able to bind to its recognition sequence, when it is localized at the edge of the core particle, but not when the recognition sequence is at the interior of the nucleosome. Remodeling of the nucleosome by the chromatin remodeling machine RSC was not sufficient to allow binding of NF-κB to its recognition sequence located in the vicinity of the nucleosome dyad, but RSC-induced histone octamer sliding allowed clearly detectable binding of NF-κB with the slid particle. Importantly, nucleosome dilution-driven removal of H2A-H2B dimer led to complete accessibility of the site located close to the dyad to NF-κB. Finally, we found that NF-κB was able to displace histone H1 and prevent its binding to nucleosome. These data provide important insight on the role of chromatin structure in the regulation of transcription of NF-κB dependent genes.
authors.affiliation: Université de Lyon, Laboratoire de Biologie Moléculaire de la Cellule, CNRS-UMR 5239, Ecole Normale Supérieure de Lyon, Lyon, France.
authors.forename: Imtiaz Nisar
authors.initials: IN
authors.lastname: Lone
authors.forename: Manu Shubhdarshan
authors.initials: MS
authors.lastname: Shukla
authors.forename: John Lalith
authors.initials: JL
authors.lastname: Charles Richard
authors.forename: Zahary Yordanov
authors.initials: ZY
authors.lastname: Peshev
authors.forename: Stefan
authors.initials: S
authors.lastname: Dimitrov
authors.forename: Dimitar
authors.initials: D
authors.lastname: Angelov
mesh_terms: D000818:Animals; D001665:Binding Sites; D002843:Chromatin / Q000235:genetics* / Q000648:ultrastructure; D004268:DNA-Binding Proteins / Q000235:genetics; D019281:Dimerization; D006657:Histones / Q000235:genetics* / Q000378:metabolism; D056245:Mi-2 Nucleosome Remodeling and Deacetylase Complex; D016328:NF-kappa B / Q000235:genetics / Q000378:metabolism*; D009707:Nucleosomes / Q000235:genetics* / Q000378:metabolism; D011485:Protein Binding; D014176:Protein Biosynthesis; D014466:Ultraviolet Rays; D014981:Xenopus / Q000235:genetics
chemical_list: D002843:Chromatin; D004268:DNA-Binding Proteins; D006657:Histones; D016328:NF-kappa B; D009707:Nucleosomes; D056245:Mi-2 Nucleosome Remodeling and Deacetylase Complex